Dr. Kaplan specializes in Indian and comparative religions with a specific focus on the Advaita Vedanta school of Hinduism and the Yogacara school of Buddhism. In addition a number of his works have been interdisciplinary engaging holography as well as the neurosciences as heuristic tools for understanding traditional philosophical issues. He has used the holographic model of David Bohm, quantum physicist, to create a model for religious pluralism in which there are more than one ultimate, not penultimate, reality (Different Paths, Different Summits: A Model for Religious Pluralism 2002 Landham: Rowman and Littlefield). In addition, he has compared the holonomic model of the brain put forth by Karl Pribram, neuroscientist, with the Advaita theory of mind (Hermeneutics, Holography, and Indian Idealism 1987Delhi: Motilal Banarsidass).

In addition to his books, Kaplan has published articles in a number of edited volumes and leading journals such as Journal of the American Academy of Religion, Philosophy East and West, Journal of Indian Philosophy, Journal of Asian Philosophy, Zygon, Journal of Religious Pluralism, International Journal of Hinduism, and Eastern Buddhist. His most recent work, "Scientific Approaches to Mysticism," appears in the Oxford Research Encyclopedia of Religion. He is currently working on a book entitled "Advaita Vedanta, the Neurosciences, and the Problem of Reductionism: What does it mean to be human?"

Dr. Kaplan received a 2002 Science and Religion Course Award from the Center for Theology and Natural Sciences. This grant was for the design and implementation of Mind, Brain and the Search for the Self - an interdisciplinary and cross-cultural approach to understanding human nature, utilizing materials from religion, philosophy, the neurosciences and the field of artificial intelligence. In 2006, Kaplan was a Senior Investigator at the Mind & Life Summer Research Institute exploring the intersections of Buddhist thought and the neurosciences. Kaplan was honored by the veteran-students of Manhattan College (Valor Association) as the first Agnes Flynn Veteran's Professor (2015).

In addition to his scholarly pursuits, Stephen Kaplan was involved for many years in New York City public school reform. He has chaired the development and establishment of an alternative elementary school - PS 51. He also received a New Vision II Award to open a public middle school in New York City. This school, the Jonas Bronck Academy, an educational collaboration with Manhattan College, originally located on the MC campus, has moved to a new location in the Bronx. Kaplan was engaged as a community organizer for over a decade working on the redevelopment of the Kingsbridge Armory, an enormous abandoned building, as a commercial, recreational, and educational center.

Most recently, he initiated a new program at Manhattan College for veteran-students—Veterans @ Ease. Working in collaboration with Warriors at Ease, a non-profit dedicated to stress-reduction for veterans, and the Sivananda Ashram and Yoga Retreat (Bahamas), all incoming veteran-students are eligible to enroll in the introductory Religious Studies course (RELS 161). This course not only introduces student to the different ways to study religion and to a variety of different religions, but these particular sections introduce the students to Indic theories of mind and yoga. With this background, each veteran-student is invited, at MC expense, to attend a 4 day retreat run by Warriors at Ease at the Sivananda Ashram and to participate in follow-up sessions on campus. The goals of this program are 1) to facilitate the successful transition to civilian-academic life, 2) to introduce stress reduction techniques for daily use, and 3) to provide avenues for veteran-students to bond with other veteran-students.